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Compare biological models, docking engines, and computational workflows side-by-side. Filter by access model, compute footprint, and category to reach an actionable decision table in under a minute.
| Attribute | Scientific ML Libraries & Supporting Tools Rosetta macromolecular modeling suiteResearch / method authors | ＋ Add tool | ||||
|---|---|---|---|---|---|---|
| Category | Scientific ML Libraries & Supporting Tools | Scientific ML Libraries & Supporting Tools | Scientific ML Libraries & Supporting Tools | Scientific ML Libraries & Supporting Tools | Research Tooling & Frameworks | — |
| Subcategory | Conventional or Statistical Baselines | Conventional or Statistical Baselines | Conventional or Statistical Baselines | Conventional or Statistical Baselines | Molecular Dynamics Engines | — |
| Company | Research / method authors | Research / method authors | Research / method authors | Research / method authors | GROMACS Development Team | — |
| Access mode | Confirm distribution and exact release | Confirm distribution and exact release | Confirm distribution and exact release | Confirm distribution and exact release | Open Source | — |
| Licence conditions | NOT_INDEPENDENTLY_AUDITED | NOT_INDEPENDENTLY_AUDITED | NOT_INDEPENDENTLY_AUDITED | NOT_INDEPENDENTLY_AUDITED | LGPL-2.1 | — |
| Compute requirements | Version and data dependent | Version and data dependent | Version and data dependent | Version and data dependent | Multi-core CPU and NVIDIA/AMD GPU for accelerated PME electrostatics | — |
| Biological application | Not recorded | Not recorded | Not recorded | Not recorded | Biomolecular dynamics, membrane transport, protein folding, and drug-target residence time | — |
| Research workflow | Not recorded | Not recorded | Not recorded | Not recorded | PDB topology generation -> energy minimization -> equilibration -> production MD trajectory | — |
| Evidence level | PEER_REVIEWED_METHOD_OR_CONFERENCE | PEER_REVIEWED_METHOD_OR_CONFERENCE | PEER_REVIEWED_METHOD_OR_CONFERENCE | PEER_REVIEWED_METHOD_OR_CONFERENCE | Cited in over 30,000 peer-reviewed biophysics publications | — |
| Commercial eligibility | NOT_INDEPENDENTLY_AUDITED | NOT_INDEPENDENTLY_AUDITED | NOT_INDEPENDENTLY_AUDITED | NOT_INDEPENDENTLY_AUDITED | Permissive open source release | — |
| Price | Verify access and licence | Verify access and licence | Verify access and licence | Verify access and licence | Free Open Source | — |
| Availability ⓘ | Method paper or official documentation | Method paper or official documentation | Method paper or official documentation | Method paper or official documentation | Available via Bioconda and source compilation | — |
| Features | MMseqs2 scientific method, Amino acid queries and reference sequence database, Sequence matches, clusters and alignment results | HMMER 3 scientific method, Query sequences or profile HMM and sequence database, Profile HMM hits and statistical homology significance | NCBI BLAST+ scientific method, Nucleotide or protein query and appropriately indexed sequence database, Local sequence alignment scores and homolog candidates | Rosetta macromolecular modeling suite scientific method, Protein structures and appropriate score function and design constraints, Energy-optimized structural/design candidates | Unrivaled simulation throughput on modern x86/ARM CPUs and NVIDIA/AMD GPUs, Comprehensive support for standard force fields (AMBER, CHARMM, OPLS, GROMOS), Free energy calculation tools for relative binding affinity and alchemical transformations, Extensive trajectory analysis utilities for root-mean-square deviation, gyration, and hydrogen bonds | — |
| Entry type | Classical/statistical scientific method | Classical/statistical scientific method | Classical/statistical scientific method | Classical/statistical scientific method | Open Source Software | — |
| AI role | NON_AI_CLASSICAL | NON_AI_CLASSICAL | NON_AI_CLASSICAL | NON_AI_PHYSICS_BASED | Physical Molecular Dynamics Simulation | — |
| Input data | Amino acid queries and reference sequence database | Query sequences or profile HMM and sequence database | Nucleotide or protein query and appropriately indexed sequence database | Protein structures and appropriate score function and design constraints | Not recorded | — |
| Output data | Sequence matches, clusters and alignment results | Profile HMM hits and statistical homology significance | Local sequence alignment scores and homolog candidates | Energy-optimized structural/design candidates | Not recorded | — |
| Validation | Published method scope; no independent BioAtlas execution or benchmark | Published method scope; no independent BioAtlas execution or benchmark | Published method scope; no independent BioAtlas execution or benchmark | Published method scope; no independent BioAtlas execution or benchmark | Not recorded | — |
| Type | Not recorded | Not recorded | Not recorded | Not recorded | Molecular dynamics simulation engine | — |
| Intended use | Not recorded | Not recorded | Not recorded | Not recorded | Not recorded | — |
| Compatibility | Not recorded | Not recorded | Not recorded | Not recorded | Not recorded | — |
| Manufacturer | Not recorded | Not recorded | Not recorded | Not recorded | GROMACS Team & KTH Royal Institute of Technology | — |
| Integration evidence | Not recorded | Not recorded | Not recorded | Not recorded | https://www.gromacs.org | — |
| Laboratory handoff | Not recorded | Not recorded | Not recorded | Not recorded | Validates dynamic conformational stability of designed protein candidates | — |